hw3

Time estimated: 3 h; taken 4 h; date started: 2023-03-18; date completed: 2023-03-30

1. Procedure

1.1 Download required file, and setting the application

• Gene list was selected and downloaded from GitHub (https://github.com/bcb420-2020/Student_Wiki/blob/master/genelist.txt). File name: genelist.txt.
• g:Profiler, a web server for functional enrichment analysis (https://biit.cs.ut.ee/gprofiler/gost)
• Data sources : Reactome, Go biologoical process, and Wiki pathways
• Multiple hypothesis testing - Benjamini hochberg

2. Analysis and interpretation

Loading the selected genelist on web g:Profiler revealed:

2.1. What is the top term returned in each data source?

• GO:BP # immune system process,
• Reactome # Immune System,
• WikiPathways # Allograft rejection

2.2. How many genes are in each of the above genesets returned? (hint, in the Detailed results tab of g:profiler results if you click on the arrows next to the stats heading you will be able to see the number of genes in a term, number of genes in your query and number of genes in your query that are also in your term).

GO:BP # 2,014 genes in the term; 414 genes in query

Reactome # 2.041 genes in the term; 334 genes in query

WikiPathways # 88 genes in the term; 291 genes in query

2.3. How many genes from our query are found in the above genesets?

GO:BP # 255 genes in both term and query

Reactome # 220 genes in both term and query

WikiPathways # 32 genes in both term and query

2.4. Change g:profiler settings so that you limit the size of the returned genesets. Make sure the returned genesets are between 5 and 200 genes in size. Did that change the results?

Yes.

GO:BP # regulation of leukocyte proliferation,

Reactome # Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell,

WikiPathways # Allograft rejection

2.5. Which of the 4 ovarian cancer expression subtypes do you think this list represents?

Since many of the top returned lists are associated with immunoregulation, it could be immunoreactive subtype.

2.6. Bonus: The top gene returned for this comparison is TFEC (ensembl gene id:ENSG00000105967). Is it found annotated in any of the pathways returned by g:profiler for our query? What terms is it associated with it g:profiler?

No.

HUGO Gene Nomenclature Committee (HGNC) reveals that TFEC is transcription factor EC.

References

Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, Vilo J. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 2019 Jul 2;47(W1):W191-W198. doi: 10.1093/nar/gkz369. PMID: 31066453; PMCID: PMC6602461.

Reimand J, Kull M, Peterson H, Hansen J, Vilo J. g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200. doi: 10.1093/nar/gkm226. Epub 2007 May 3. PMID: 17478515; PMCID: PMC1933153.

Reimand J, Arak T, Vilo J. g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 2011 Jul;39(Web Server issue):W307-15. doi: 10.1093/nar/gkr378. Epub 2011 Jun 6. PMID: 21646343; PMCID: PMC3125778.

Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, Vilo J. g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9. doi: 10.1093/nar/gkw199. Epub 2016 Apr 20. PMID: 27098042; PMCID: PMC4987867.

Steipe, B. Modified: Isserlin, R. (2020-01-02) BCB420 - Computational System Biology. Retrieved 2023-01-20 from: BCB420 Winter 2023 course materials